The technology disclosed relates to methods and systems that can be used to reduce visible artifacts know as mura. In particular, it relates to producing alignment marks by physically modifying appearance of a layer of exposure or radiation sensitive material on a workpiece, then using those alignment marks or transferred direct or inverted images of those marks to realign a writing coordinate system between exposure writing passes, following physical movement of the workpiece within the writing system. The physical modifications described include mechanically pressing a mark into the layer, using a laser to ash or ablate the layer, or applying an ink or other substance to the surface of the laser.